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Turner 1999

Exterior Loop

Example

 exterior loop example structure

Free Energy Change

Prediction of Stacking

The predicted stacking configuration is the one with lowest free energy change. There are two possible configurations.

Configuration 1:

Helix 1 with 5' dangling U, Helix 2 with 3' dangling C, and Helix 3 with a GG mismatch

∆G°37 = ∆G°37(AU with 5' dangling U) + ∆G°37(CG with 3' dangling C) + ∆G°37(CG with GG mismatch)

∆G°37 = –0.2 kcal/mol 0.8 kcal/mol – 1.6 kcal/mol

∆G°37 = –2.6 kcal/mol

Configuration 2:

Helix 1 in a flush coaxial stack with Helix 2 and Helix 3 with a GG mismatch

∆G°37 = ∆G°37(coaxial stack of AU followed by GC) + ∆G°37(CG with GG mismatch)

∆G°37 = –2.08 kcal/mol 1.6 kcal/mol

∆G°37 = –3.7 kcal/mol

Therefore, configuration 2, -3.7 kcal/mol, is the predicted free energy change.